Contacts of the helix formed by residues 207 - 220 (chain C) in PDB entry 1H25
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C LEU* 3.7 13.0 - - - -
205C GLY 3.3 2.0 + - - -
206C ASP* 1.3 81.2 - - - +
208C GLU* 1.3 67.3 + - - +
209C ILE* 2.8 27.5 - - - +
210C ASP* 3.0 5.8 + - - +
211C GLN* 2.9 21.7 + - - +
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C HIS* 5.8 4.1 - - - -
166C LEU* 4.2 4.4 - - + +
169C ARG* 4.2 17.0 + - - +
173C ILE 5.1 0.3 - - - +
174C LEU* 3.4 43.2 - - + +
207C SER* 1.3 74.0 - - - +
209C ILE* 1.3 62.7 + - - +
211C GLN* 3.3 4.7 + - - +
212C LEU* 3.1 29.4 + - + +
235C ASP* 5.3 2.8 - - - +
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Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C SER* 2.8 27.4 - - - +
208C GLU* 1.3 76.6 - - - +
210C ASP* 1.3 61.7 + - + +
212C LEU* 3.2 16.7 + - + +
213C PHE* 3.0 63.3 + - + -
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Residues in contact with ASP 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ASP* 2.8 35.7 + - + +
207C SER* 3.0 13.3 + - - +
209C ILE* 1.3 81.7 - - + +
211C GLN* 1.3 59.4 + - - +
213C PHE* 3.8 15.5 - - + +
214C ARG* 2.6 60.6 + - - +
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Residues in contact with GLN 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C LEU* 3.5 35.2 + - + +
167C TRP* 3.4 14.2 + - - -
169C ARG 4.9 1.2 + - - +
174C LEU* 3.6 20.0 - - + -
203C PHE* 2.6 49.7 + - - +
205C GLY* 2.7 20.9 + - - -
207C SER 2.9 11.5 + - - +
208C GLU 3.3 10.5 - - - +
210C ASP* 1.3 77.0 + - - +
212C LEU* 1.3 65.5 + - - +
214C ARG* 3.2 4.9 + - - +
215C ILE* 3.1 35.7 + - + +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PRO* 4.6 8.1 - - + -
174C LEU* 3.4 38.1 - - + +
175C LEU* 3.6 30.7 - - + -
208C GLU* 3.1 18.2 + - + +
209C ILE* 3.5 16.2 - - + +
211C GLN* 1.3 81.1 - - - +
213C PHE* 1.3 63.8 + - + +
215C ILE* 3.0 8.0 + - + +
216C PHE* 2.9 56.8 + - + -
235C ASP* 5.6 2.9 - - + +
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ILE* 3.0 52.2 + - + +
210C ASP* 3.8 16.6 - - + +
211C GLN 3.3 0.2 - - - -
212C LEU* 1.3 76.2 - - + +
214C ARG* 1.3 63.4 + - + +
215C ILE 3.0 0.2 + - - -
216C PHE* 3.2 18.1 + + + +
217C ARG* 3.0 27.9 + - - +
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Residues in contact with ARG 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C PHE* 3.8 17.3 - - + -
204C PRO* 3.2 32.7 + - - +
205C GLY* 3.5 16.6 - - - +
206C ASP* 3.5 17.2 + - - -
210C ASP* 2.6 48.4 + - - +
211C GLN* 3.2 5.8 + - - +
213C PHE* 1.3 76.4 - - + +
215C ILE* 1.3 56.9 + - - +
217C ARG* 3.1 57.0 + - - +
218C THR* 3.2 15.2 + - - -
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Residues in contact with ILE 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ARG 4.4 2.2 - - - +
171C PRO* 5.0 5.2 - - + -
174C LEU* 4.2 13.7 - - + -
187C TRP* 4.0 21.5 - - + -
203C PHE* 3.5 28.7 - - + -
211C GLN* 3.1 38.5 + - + +
212C LEU* 3.0 9.3 + - + +
213C PHE 3.0 0.6 - - - -
214C ARG* 1.3 76.0 - - - +
216C PHE* 1.3 60.2 + - + +
217C ARG 3.2 1.3 - - - -
218C THR 3.0 0.5 + - - -
219C LEU* 2.7 57.6 + - + +
269C TYR* 3.4 17.8 + - + +
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Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C PRO* 5.6 4.0 - - + -
175C LEU* 5.2 11.7 - - + -
212C LEU* 2.9 59.0 + - + +
213C PHE* 3.9 19.5 - + + +
215C ILE* 1.3 78.7 - - + +
217C ARG* 1.3 56.0 + - - +
220C GLY* 2.5 32.2 + - - -
221C THR* 3.0 33.6 + - + +
222C PRO* 3.3 37.2 - - + -
269C TYR* 3.8 13.0 - + - -
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Residues in contact with ARG 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU 5.6 3.0 + - - -
204C PRO* 5.5 3.2 - - - +
213C PHE 3.0 12.0 + - - +
214C ARG* 3.1 63.5 + - - +
216C PHE* 1.3 77.1 - - - +
218C THR* 1.3 69.5 + - - +
220C GLY* 4.2 1.4 + - - -
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Residues in contact with THR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU* 4.7 5.3 + - + -
203C PHE* 4.0 15.9 - - + -
214C ARG 3.2 17.9 + - - -
215C ILE 3.0 2.5 + - - -
217C ARG* 1.3 95.6 + - - +
219C LEU* 1.3 74.2 + - + +
220C GLY 3.3 0.2 - - - -
251C VAL* 4.0 36.8 - - + +
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C TRP* 3.9 15.3 - - + -
202C LEU* 5.8 0.2 - - + -
203C PHE* 3.8 19.7 - - + -
215C ILE* 2.7 36.6 + - + +
218C THR* 1.3 90.0 - - + +
220C GLY* 1.3 64.7 + - - +
267C LEU* 4.2 30.7 - - + +
269C TYR* 2.9 25.3 + - + +
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Residues in contact with GLY 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C PHE 2.5 21.6 + - - -
217C ARG 4.2 1.5 + - - -
218C THR 3.3 2.8 + - - -
219C LEU* 1.3 75.3 - - - +
221C THR* 1.3 68.8 + - - +
269C TYR* 2.6 25.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il